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<h4> Setup ICA Analysis </h4>

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<p> Before entering the parameters using <em>Setup ICA</em>, figure out how many 
data-sets you are analyzing. Use batch script to run the analysis or entering 
design matrix (required during temporal sorting) for large data-sets. </p>
<p><em>Setup ICA Analysis</em> step involves entering parameters for the group 
ICA analysis. When you click <em>Setup ICA Analysis</em> button, a figure window 
will open to select the analysis output directory. After the directory is 
selected, parameter options figure (Figure 1) will be displayed. The parameters 
in the figure will be explained step by step and for additional information 
click on the link highlighted. Some of the user interface controls are shielded 
from the user. These controls will be shown when you click <a href="icatb_setup_ica_defaults.htm">
SetupICA-Defaults</a> menu. </p>
<p class="style1"> Figure 1: Initial Parameter Select Window </p>

<p class="style1"> <img src="images/icatb_setup_ica_initial.jpg"> </p>

<p> <b> Main User Interface Controls:</b></p>
  <dl>
  <dt>Enter name (Prefix) of Output Files</dt>
  <dd>Prefix string to all the output files created by the GIFT.</dd>
  <dt>Have You Selected The fMRI Data Files? </dt>
  <dd>Select<ul>
    <li>Functional data needs to be selected. When you click this button,&nbsp; you 
	can select the data using two methods. 
    <ul>
    <li> Method one can be used to select large data-sets. If your data is in 
	one folder and have a common file pattern, specify the filter pattern and 
	select the appropriate answer for the question &quot;Are session folders inside 
	subject folders?&quot;. See <a href="icatb_select_data.htm">screen shots</a> 
	of the example data selection.</li>

	<li> Method two can be used to select data-sets that do not have data in one 
	folder or have a common file pattern. For large data-sets use batch script 
	for entering the data. </li>	
	</ul>
	
	<li> After selecting the data files, the information is stored in a file 
	with suffix &quot;Subject.mat&quot; and the button will be changed to pop up window 
	with 'Yes' and 'No' as options. The explanation for 'Yes' is explained 
	below. 'No' is used if you want to select the data files again.</li>
  </ul>
  </dd>
  <dd>Yes
  <ul>
    <li>'Yes' option will be shown&nbsp; if you have already selected the data files 
	based on the output prefix entered.</li>
    <li>The data reduction parameters are updated and the estimate components 
	popup window is enabled.</li>
    <li> If the data is entered for the first time, the numbers for the 
	principal components are set to 20. </li>
  </ul>
  </dd>
  <dt>Do you want to estimate the number of independent components? </dt>
  <dd>Yes
  <ul>
    <li>Components are estimated from the fMRI data (
    <a target="_self" href="icatb_references.htm">[5] </a>) using the MDL 
	criteria.
    </li>
    <li>Mean of the estimated components for all data-sets is taken when you use 
	all subjects to estimate the components and the statistics are performed. 
	After the statistics are calculated, all the information with a <i>Plot </i>
    button will be shown in a dialog box. The mean of MDL plot for all data-sets 
	will be shown when you click the <i>
    Plot </i>button.</li>
    <li>When a particular subject's session is selected the independent 
	components are estimated and the plot of MDL is shown when clicked on the <i>
	Plot</i> 
    button in the dialog box. </li>
  </ul>
  </dd>
</dl>
<dl>
  <dt>Number of IC</dt>
  <dd>Number of independent components extracted from the data.</dd>
  <dt>Do You Want to Autofill Data Reduction Values?</dt>
  <dd>Numbers for principal components are auto-filled. You can take a look at 
  these parameters by clicking on &quot;Setup ICA-Defaults&quot; menu.</dd>
  <dt>Which algorithm do you want to use? </dt>
  <dd>ICA algorithms like Infomax, FastICA, Erica, Simbec, JADE OPAC, Evd, 
  Amuse, SDD ICA, Semi-blind ICA, Constrained ICA (Spatial), Radical ICA , Combi, 
  ICA-EBM and FBSS are incorporated. </dd>
  <dd><b>Note: </b>ICA options window (Figure 2) will popup depending on the 
  algorithm selected. Presently, ICA options are available for Infomax, FastICA, 
  SDD ICA, Semi-blind ICA and Constrained ICA (Spatial) . ICA options window can 
  be turned off by replacing variable ICAOPTIONS_WINDOW_DISPLAY to 'off' (<a href="icatb_defaults.htm">Defaults</a>).</dd>
	<dt>Which Group ICA Analysis You Want To Use? </dt>
	<dd> Options are 'Regular' and 'ICASSO'. When you select 'ICASSO', ICA is 
	run several times and the best estimate for each component is used. </dd>
	

</dl>

<p class="style1">Figure 2: ICA Options Window</p>
<p class="style1"> <img src="images/icatb_ica_options.jpg"> </p>

<p class="style1">Figure 3: Completed Parameter Select Window</p>
<p class="style1"> <img border="0" src="images/icatb_setup_ica_final.jpg"></p>

Figure 3 shows the completed parameters. Press <i>Done</i> button once the 
answers for the parameters are entered. Parameter file for the analysis is 
created in the working directory with the suffix '_ica_parameter_info.mat' 

<p>After the parameters are saved in a file, use <i><a href="icatb_run_analysis.htm">
Run Analysis</a></i> button to run the analysis.</p>

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